+Open data
-Basic information
Entry | Database: PDB / ID: 3g56 | ||||||
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Title | Structure of the macrolide biosensor protein, MphR(A) | ||||||
Components | Regulator of macrolide 2'-phosphotransferase I | ||||||
Keywords | DNA BINDING PROTEIN / macrolide antibiotic / repressor / biosensor / erythromycin / Streptomyces / natural products / biosynthesis / DNA-binding / Transcription / Transcription regulation | ||||||
Function / homology | Function and homology information transferase activity / transcription cis-regulatory region binding / DNA-binding transcription factor activity Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Zheng, J. / Sagar, V. / Smolinsky, A. / Bourke, C. / LaRonde-LeBlanc, N. / Cropp, T.A. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2009 Title: Structure and function of the macrolide biosensor protein, MphR(A), with and without erythromycin Authors: Zheng, J. / Sagar, V. / Smolinsky, A. / Bourke, C. / LaRonde-LeBlanc, N. / Cropp, T.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3g56.cif.gz | 82.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3g56.ent.gz | 62.5 KB | Display | PDB format |
PDBx/mmJSON format | 3g56.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3g56_validation.pdf.gz | 462.2 KB | Display | wwPDB validaton report |
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Full document | 3g56_full_validation.pdf.gz | 475.7 KB | Display | |
Data in XML | 3g56_validation.xml.gz | 17.7 KB | Display | |
Data in CIF | 3g56_validation.cif.gz | 23.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g5/3g56 ftp://data.pdbj.org/pub/pdb/validation_reports/g5/3g56 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 21710.186 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: mphR(A) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9EVJ6 #2: Chemical | ChemComp-EDO / | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.12 Å3/Da / Density % sol: 42.04 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 18%-22% (W/V) PEG 3350, 0.2M ammonium acetate, 0.1M Bis-Tris, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9795 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 1, 2008 |
Radiation | Monochromator: Konzu HLD8-24 filter monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→29.27 Å / Num. all: 20014 / Num. obs: 19704 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 2.1→2.18 Å / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→29.27 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.914 / SU B: 15.261 / SU ML: 0.196 / Cross valid method: THROUGHOUT / ESU R: 0.274 / ESU R Free: 0.231 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 49.083 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→29.27 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.101→2.156 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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